In-Silico Identification of Putative p53 Transcription Factor DNA-Binding Sites and Detection of hnRNP Genes Regulated by p53

Dutta, Avirup; Chatterjee, Raghunath; Roychoudhury, Paromita; Roy, Patanjal; Chaudhuri, Keya
June 2010
IUP Journal of Biotechnology;Jun2010, Vol. 4 Issue 2, p7
Academic Journal
An evolutionary ancient transcription factor p53 coordinates diverse cellular responses to stress and damage and plays an emerging role in various physiological processes by regulating the expression of a number of genes of diverse families and pathways. The p53 DNA-binding motif consists of a consensus region of around 34 bases comprising two inverted palindromic repeats separated by a variable spacer region. An algorithm was developed to identify putative binding elements on 503 selected human genes in the promoter regions and subsequently scored using a reference weight matrix. The genes chosen were loosely classified into seven different biological pathways or families related to various cellular and metabolic pathways. About 124 genes were identified as potential p53 targets which had scores above a theoretical cut-off value. A group of hnRNP genes were tested by semiquantative reverse transcription (RT) PCR analysis for p53 responsiveness. Semiquantitative RT-PCR experiments were performed in p53 null cell line H1299 and in p53 transfected H1299 cells. Four out of six genes responded to the presence of p53.


Related Articles

  • Binding of the winged-helix transcription factor HNF3 to a linker histone site on the nucleosome. Cirillo, Lisa A.; McPherson, Clifton E.; Bossard, Pascale; Stevens, Kimberly; Cherian, Sindhu; Shim, Eun Yong; Clark, Kirk L.; Burley, Stephen K.; Zaret, Kenneth S. // EMBO Journal;1/1/98, Vol. 17 Issue 1, p244 

    The transcription factor HNF3 and linker histones H1 and H5 possess winged-helix DNA-binding domains, yet HNF3 and other fork head-related proteins activate genes during development whereas linker histones compact DNA in chromatin and repress gene expression. We compared how the two classes of...

  • Identification of a new class of PAX3-FKHR target promoters: a role of the Pax3 paired box DNA binding domain. Zhang, L.; Wang, C. // Oncogene;3/8/2007, Vol. 26 Issue 11, p1595 

    Alveolar rhabdomyosarcoma (aRMS), an aggressive skeletal muscle cancer, carries a unique t(2;13) chromosomal translocation resulting in the formation of a chimeric transcription factor PAX3-FKHR. This fusion protein contains the intact DNA-binding domains (PD: paired box binding domain; HD:...

  • Co-expression of adjacent genes in yeast cannot be simply attributed to shared regulatory system. Huai-Kuang Tsai; Su, Cindy PC; Mei-Yeh J Lu; Ching-Hua Shih; Wang, Daryi // BMC Genomics;2007, Vol. 8, p352 

    Background: Adjacent gene pairs in the yeast genome have a tendency to express concurrently. Sharing of regulatory elements within the intergenic region of those adjacent gene pairs was often considered the major mechanism responsible for such co-expression. However, it is still in debate to...

  • A molecular modeling study of inhibitors of nuclear factor kappa-B (p50) – DNA binding. Pande, Vineet; Sharma, Rakesh K.; Inoue, Jun-Ichiro; Otsuka, Masami; Ramos, Maria J. // Journal of Computer-Aided Molecular Design;Dec2003, Vol. 17 Issue 12, p825 

    Nuclear Factor-kappa B (NF-κB) is an inducible transcription factor of the Rel family, and is sequestered in the cytoplasm by the IκB family of proteins. NF-κB can exist in several dimeric forms, but the p50/p65 heterodimer is the predominant one. Activation of NF-κB by a range of...

  • Islet-Enriched Transcription Factors Synergistically Activate Transcription of the Gene Encoding the Autoantigen IGRP. Martin, Cyrus C.; Flemming, Brian P.; Wang, Yingda; Oeser, James K.; O'Brien, Richard M. // Diabetes;Jun2007 Supplement 1, Vol. 56, pA430 

    Islet-specific glucose-6-phosphatase catalytic subunit-related protein (IGRP) is selectively expressed in islet beta cells and is a major autoantigen in both mouse and human type I diabetes. It is possible that suppression oflGRP gene transcription may prevent or delay the progression of this...

  • Assessing the Effects of Symmetry on Motif Discovery and Modeling. Motlhabi, Lala M.; Stormo, Gary D. // PLoS ONE;2011, Vol. 6 Issue 9, p1 

    Background: Identifying the DNA binding sites for transcription factors is a key task in modeling the gene regulatory network of a cell. Predicting DNA binding sites computationally suffers from high false positives and false negatives due to various contributing factors, including the...

  • Chromosome-Biased Binding and Gene Regulation by the Caenorhabditis elegans DRM Complex. Tabuchi, Tomoko M.; Deplancke, Bart; Osato, Naoki; Zhu, Lihua J.; Barrasa, M. Inmaculada; Harrison, Melissa M.; Horvitz, H. Robert; Walhout, Albertha J. M.; Hagstrom, Kirsten A. // PLoS Genetics;May2011, Vol. 7 Issue 5, Special section p1 

    DRM is a conserved transcription factor complex that includes E2F/DP and pRB family proteins and plays important roles in development and cancer. Here we describe new aspects of DRM binding and function revealed through genome-wide analyses of the Caenorhabditis elegans DRM subunit LIN-54. We...

  • Transcriptional responses to ionizing radiation reveal that p53R2 protects against radiation-induced mutagenesis in human lymphoblastoid cells. Tsai, M.-H.; Chen, X.; Chandramouli, G. V. R.; Chen, Y.; Yan, H.; Zhao, S.; Keng, P.; Liber, H. L.; Coleman, C. N.; Mitchell, J. B.; Chuang, E. Y. // Oncogene;1/26/2006, Vol. 25 Issue 4, p622 

    The p53 protein has been implicated in multiple cellular responses related to DNA damage. Alterations in any of these cellular responses could be related to increased genomic instability. Our previous study has shown that mutations in p53 lead to hypermutability to ionizing radiation. To...

  • Modulation of Tcf3 repressor complex composition regulates cdx4 expression in zebrafish. Ro, Hyunju; Dawid, Igor B // EMBO Journal;7/20/2011, Vol. 30 Issue 14, p2894 

    The caudal homeobox (cdx) gene family is critical for specification of caudal body formation and erythropoiesis. In zebrafish, cdx4 expression is controlled by the Wnt pathway, but the molecular mechanism of this regulation is not fully understood. Here, we provide evidence that Tcf3 suppresses...


Read the Article


Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics